Again, I suck with the search function. Pardons if this has been posted.
After you invade a planet, the planetary population will reflect the remaining total troops on the planet. However, you only "use up" any transports who have some or all of their troops killed. Any remaining whole ship's compliments will cause the trasports themselves to remain in orbit, and will be FULL.
That means if I invade with 4k troops (4 billion, in other words), and only 500 die, then the population of the planet will be 3.5 billion. AND, I will have 3 transports with 3K (3 billion) troops STILL on them. Say hello to tax revenue baby!
Its the magic of replication!!!

EDIT pardon the multiple posts, had a forum error